Freesurfer

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30070 discussions

Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz
by Gamaliz 25 Apr '17

25 Apr '17

I wrote an algorithm which uses the number of pixels per region in the aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number of pixels to match very closely the value of the volume; as each pixel represents a 1 mm3 cube.(I did the same for cortical volume and got a similar result, with an even larger discrepancy). The aseg.stats file lists the nVoxel value, and it is basically the volume rounded up. here are some sample values for subcortical regions: Left-Lateral-Ventricle Volume (mm3): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899 Pretty much the values are close to the volume, but different enough to be significant. I wonder why this discrepancy.

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Additional processing flags when using the longitudinal pipeline
by Gustav Mårtensson 25 Apr '17

25 Apr '17

Hi, I have a question regarding the longitudinal pipeline. We are following the workflow summary as outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, essentially: 1. recon-all -all -s <tpNid> -i path_to_tpN_dcm 2. recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all 3. recon-all -long <tpNid> <templateid> -all We tend to run -all -mprage -qcache -hippocampal-subfields-T1 -brainstem-structures in our cross-sectional process. Should we use all (or part of) these options for step 2 and 3? We are running on Ubuntu 16.04 LTS with FS version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. Thank you for your help! Gustav Mårtensson -- Gustav Mårtensson | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet ___________________________________ Karolinska Institutet – a medical university

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summary 500 samples FS results
by shi yao wang 24 Apr '17

24 Apr '17

Dear FS expert, We have running around 500 samples by FS. I am wondering if there are easy way to summary these data. i.e., generate mean of cortical thickness. thanks Shiyao

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Re: [Freesurfer] volume in native space of .vtk file in mni152 space
by Antonin Skoch 24 Apr '17

24 Apr '17

Dear Corinna, I am not sure what is (or whether is) something wrong with your commands, but in any case I would be cautious of interpretation of results using such method, mainly from following reasons: 1. mni152reg uses 12 DOF whole-brain registration. You cannot expect to get perfect alignment of subcortical regions using such crude transform. To obtain more precise transform, I would use either registration targeted specifically to subcortical regions (e.g. using first_flirt in FSL, which is, however, still affine only), or use mri_cvs_register. 2. Due to no reasonable contrast within thalamus to allow to distinguish the nuclei using even state-of-the-art MR imaging, such registration-based atlas method would by necessity be a simple transfer of predefined atlas onto the subject space, with no information to guide the alignment within the thalamus itself (it would basically be a best-guiess of where these nuclei might be, with no scope for subject-specific refinement). Antonin Skoch Hi al, Just wondering if anyone has any suggestionsto my previous question as to why the volume from mni152 space would be rotated, even though the MNI152 to subject T1 alignment looks good? As a recap, here are my commands: mni152reg --s ${subject} --1 tkregister2 --mov ${subj_dir}/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz --reg ${reg_file} mri_vol2vol --mov ${subj_dir}/mri/orig.mgz --targ /home/Documents/thalamus/AtlasMNI152/left-vols-1mm/global.nii.gz --reg ${reg_file} --inv --o ${out_dir}/lh_global.nii.gz tkmedit -f subject/mri/orig.mgz -aux ${out_dir}/lh_global.nii.gz -ov ${out_dir}/lh_global.nii.gz -fminmax .5 1

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freesurferstats2table_bash
by shi yao wang 24 Apr '17

24 Apr '17

Dear FS experts: Would you pls provide freesurferstats2table_bash script? The link of http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table does not work. thanks Shiyao

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How are Vertex RAS coordinates calculated in TKsurfer
by Zhiliang Long 24 Apr '17

24 Apr '17

Dear FS experts: I am studying the coordinate system in FS. I met a problem that confused me. I run tksurfer: tksurfer fsaverage lh inflated. Then I chose a point on surface. It showed that the Vertex Index is 80321, and the Vertex RAS is (-38.53 9.05 40.01). I thought that the Vertex RAS is just obtained from the lh.inflated file. But I run: mris_info --v 80321 .\fsaverage\surf\lh.inflated. It showed that coordinate is (-18.4 40.8 32.7). I have no idea that how the Vertex RAS is calculated in Tksurfer. Maybe is there a transform matrix between the two coordinates ? If so, how can i get the transform matrix ? Best, Zhiliang

2 1

Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
by Antonin Skoch 24 Apr '17

24 Apr '17

Dear experts, I am sending just one more example to illustrate issue with white surface estimation in v6.0. See the attached screenshots: In v6.0 there seems to be insufficient contrast in brain.finalsurfs.mgz, so the white surface is leaking at three spots dramatically outwards towards pial surface. The white surface in v5.3 looks much more anatomically relevant in the same spot. Could you please comment on how to avoid such issues in v.6.0? Regards, Antonin Skoch

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Cognomics conference: poster and advertisement
by X K 24 Apr '17

24 Apr '17

This message contained a link to a web site whose IP address has recently been associated with malicious activity. Due to that activity the site is not accessible from within the Partners Network. The link has been modified in the message below. If you feel this is an error please contact the IS Service Desk and open a ticket with the network security - phs assignment group. IS Service Desk numbers BWH 617-732-5927 BWH-RICS 617-525-0848 DFCI 617-632-3399 FALK 617-983-7454 LCC 857-307-4150 MCL 781-416-8940 MGH 617-726-5085 NHP 617-643-2020 NSMC 978-354-2014 NWH 617-243-6001 PCHI 781-433-3757 PHH 617-726-0790 PHS 617-726-5085 SRH 617-952-5555 ********************************* *FYI:* Dear all, We are happy to announce the COGNOMICS Conference 2017 with the topic of “Neurogenomics: the road ahead”! This conference will be held on the 7th and 8th of September 2017 at the Donders Institute for Brain, Cognition and Behaviour in Nijmegen, the Netherlands. The program includes a keynote lecture by the world-leading neuroscientist and founder of the worldwide ENIGMA Consortium, Paul Thompson (University of Southern California), and several invited talks by top-researchers in the field, covering the state-of-the-art on imaging genetics and novel developments in phenotyping and genomics. It also includes a panel discussion on the future of imaging genetics and several stimulating oral and poster sessions. Participants will compete for a Best Poster award. Please find the program, as well as a further information about registration on our website BLOCKEDcognomics[.]nlBLOCKED. We invite you and your colleagues to submit abstracts for oral and poster presentations (max. 250 words excluding the title, author names, and references). Abstract submission deadline is June 15, 2017 Max number of participants is 120, so sign-up now! We hope to see you in September! Kind regards, on behalf of the Cognomics Board Barbara Franke Professor of Molecular Psychiatry Radboud University Medical Center Nijmegen Dr. Xiangzhen Kong (孔祥祯) Language and Genetics Department, Max Planck Institute for Psycholinguistics http://www.mpi.nl/people/kong-xiangzhen

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Weighted Average of Cortical Thickness
by Michael Kranz 24 Apr '17

24 Apr '17

Hi, I had 2 questions relating to measuring global mean cortical thickness with the weighting factor of surface area bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea) 1.) If this weighting is recommended, then shouldn't it be performed for each vertex in an exploratory whole brain group analyses (e.g., for one vertex in left hemi: lh.thickness*lh.surfarea)/(lh.surfarea). 2.) Are there any references that come to mind to cite in regards to this normalization technique? I see that this following paper uses normalization (but was wondering if you would recommend any others): Vuoksimaa, E., Panizzon, M. S., Chen, C.-H., Fiecas, M., Eyler, L. T., Fennema-Notestine, C., … Kremen, W. S. (2015). The Genetic Association Between Neocortical Volume and General Cognitive Ability Is Driven by Global Surface Area Rather Than Thickness. *Cerebral Cortex (New York, NY)* , *25*(8), 2127–2137. http://doi.org/10.1093/cercor/bhu018 Best, Mike

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volume in native space of .vtk file in mni152 space
by Corinna Bauer 23 Apr '17

23 Apr '17

Dear all, I have a series of .vtk files in MNI152 1mm space from an external thalamus atlas outlining specific thalamic nuclei. I would like to put these into native subject space and calculate the volume from each nuclei. I would imagine that I would do the following: 1. run mni152reg --s --1 on each subject 2. mri_vol2vol --mov mni152space_atlas_file.nii.gz -- targ subject/mri/orig.mgz --reg subject/mri/mni152.orig.mgz.reg --inv --o newoutputfile_subject_space But then I am not certain how to calculate the volume of the new output file. Suggestions? Thanks! Corinna

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